// Created by libAntimony v2.8.0
model *Nazaret2009_TCA_RC_ATP()

  // Compartments and Species:
  compartment cytoplasm, mitochondrion;
  species $ADP in mitochondrion, ATP in mitochondrion, $H in mitochondrion;
  species $He in cytoplasm, NAD in mitochondrion, $NADH in mitochondrion;
  species AcCoA in mitochondrion, KG in mitochondrion, Cit in mitochondrion;
  species OAA in mitochondrion, $O2 in mitochondrion, $iP in mitochondrion;
  species Pyr in mitochondrion, $H2O in mitochondrion;

  // Assignment Rules:
  ADP := At_ - ATP;
  NADH := Nt - NAD;
  ATPcrit := At_/(1 + exp((-3*DeltaGtransport)/(R*T))/(Kapp*iP));
  DeltaGtransport := 1.2*F*DeltaPsi;
  Jresp := (kresp*((Nt - NAD)/((K + Nt) - NAD)))/(1 + exp(a*(DeltaPsi - DeltaPsim)));
  JATP := kATP*(2/(1 + exp(b*(ATP - ATPcrit))) - 1);
  Jleak := kleak*DeltaPsi;
  JANT := kANT*ATP;

  // Rate Rules:
  DeltaPsi' = (10*Jresp - 3*JATP - Jleak - JANT)/C;

  // Reactions:
  v1:  => Pyr; mitochondrion*v1_k1;
  v2: Pyr + NAD => AcCoA + $NADH; mitochondrion*v2_k2*Pyr*NAD;
  v3: OAA + AcCoA => Cit; mitochondrion*v3_k3*OAA*AcCoA;
  v4: Cit + NAD => KG + $NADH; mitochondrion*v4_k4*Cit*NAD;
  v5: KG + $ADP + 2NAD => OAA + ATP + 2$NADH; mitochondrion*v5_k5*KG*NAD*(At_ - ATP);
  v6: OAA -> KG; mitochondrion*v6_k6*(OAA - KG/v6_Keq);
  v7: Pyr + ATP => OAA + $ADP; mitochondrion*v7_k7*Pyr*ATP;
  v8: OAA => ; mitochondrion*v8_k8*OAA;
  vresp: $NADH + 0.5$O2 + 11$H => NAD + $H2O + 10$He; mitochondrion*Jresp;
  vATP: $ADP + $iP + 3$He -> ATP + $H2O + 3$H; mitochondrion*JATP;
  vANT: ATP => $ADP; mitochondrion*JANT;
  vleak: $He => $H; mitochondrion*Jleak;

  // Species initializations:
  ATP = 3.536;
  H = 1;
  He = 1;
  NAD = 0.856;
  AcCoA = 0.063;
  KG = 0.225;
  Cit = 0.44;
  OAA = 0.005;
  O2 = 1;
  iP = 2.44;
  Pyr = 0.154;
  H2O = 1;

  // Compartment initializations:
  cytoplasm = 1;
  mitochondrion = 1;

  // Variable initializations:
  At_ = 4.16;
  At_ has mM;
  Nt = 1.07;
  Nt has mM;
  ATPcrit has mM;
  DeltaGtransport has mJ_per_mol;
  R = 8314;
  R has mJ_per_mol_per_K;
  T = 298;
  T has kelvin;
  Kapp = 4.4e-009;
  Kapp has per_mM;
  C = 6.75e-006;
  C has mM_per_mV;
  F = 96485;
  F has C_per_mol;
  DeltaPsi = 150;
  DeltaPsi has mV;
  Jresp has mM_per_s;
  JATP has mM_per_s;
  Jleak has mM_per_s;
  JANT has mM_per_s;
  DeltaPsim = 150;
  DeltaPsim has mV;
  kANT = 0.05387;
  kANT has per_s;
  kATP = 131.9;
  kATP has mM_per_s;
  b = 0.004;
  b has per_mM;
  kleak = 0.000426;
  kleak has mM_per_s_per_mV;
  kresp = 2.5;
  kresp has mM_per_s;
  K = 2;
  K has mM;
  a = 0.1;
  a has per_mV;
  v1_k1 = 0.038;
  v1_k1 has mM_per_s;
  v2_k2 = 0.152;
  v2_k2 has per_mM_per_s;
  v3_k3 = 57.142;
  v3_k3 has per_mM_per_s;
  v4_k4 = 0.053;
  v4_k4 has per_mM_per_s;
  v5_k5 = 0.082361;
  v5_k5 has per_mM_squared_per_s;
  v6_k6 = 0.0032;
  v6_k6 has per_s;
  v6_Keq = 0.3975;
  v6_Keq has dimensionless;
  v7_k7 = 0.04;
  v7_k7 has per_mM_per_s;
  v8_k8 = 3.6;
  v8_k8 has per_s;

  // Other declarations:
  var ATPcrit, DeltaGtransport, DeltaPsi, Jresp, JATP, Jleak, JANT;
  const cytoplasm, mitochondrion, At_, Nt, R, T, Kapp, C, F, DeltaPsim, kANT;
  const kATP, b, kleak, kresp, K, a;

  // Unit definitions:
  unit substance = 1e-3 mole;
  unit C_per_mol = 1e1 coulomb / 1e1 mole;
  unit mJ_per_mol_per_K = 1e-3 joule / (1e1 mole * 1e1 kelvin);
  unit mJ_per_mol = 1e-3 joule / 1e1 mole;
  unit mM = 1e-3 mole / 1e1 litre;
  unit mM_per_mV = 1e-3 mole / (1e1 litre * 1e-3 volt);
  unit mM_per_s = 1e-3 mole / (1e1 litre * 1e1 second);
  unit mM_per_s_per_mV = 1e-3 mole / (1e1 litre * 1e1 second * 1e-3 volt);
  unit mV = 1e-3 volt;
  unit per_mM = 1e1 litre / 1e-3 mole;
  unit per_mM_per_s = 1e1 litre / (1e-3 mole * 1e1 second);
  unit per_mM_squared_per_s = (1e1 litre)^2 / ((1e-3 mole)^2 * 1e1 second);
  unit per_mV = 1 / 1e-3 volt;
  unit per_s = 1 / 1e1 second;

  // Display Names:
  C_per_mol is "coulomb per mole";
  mJ_per_mol_per_K is "milliJoule per mole per Kelvin";
  mJ_per_mol is "milliJoules per mole";
  mM is "millimolar";
  mM_per_mV is "millimolar per millivolt";
  mM_per_s is "millimolar per second";
  mM_per_s_per_mV is "millimolar per second per millivolt";
  mV is "millivolt";
  per_mM is "per mM";
  per_mM_per_s is "per millimolar per second";
  per_mM_squared_per_s is "per millimolar squared per second";
  per_mV is "per millivolt";
  per_s is "per second";
  mitochondrion is "mitochondrial matrix";
  H is "H+";
  He is "H+";
  NAD is "NAD(+)";
  AcCoA is "acetyl-CoA";
  KG is "alpha-ketoglutarate";
  Cit is "citrate";
  OAA is "oxaloacetate";
  O2 is "oxygen";
  iP is "phosphate";
  Pyr is "pyruvate";
  H2O is "water";
  R is "gas constant";
  T is "absolute temperature";
  F is "Faraday constant";
end